MPRAsnakeflow experiment QC report

Good Spearman correlation across replicates!

The data has a good Spearman correlations across replicates using a barcode threshold per oligo of 10! Spearman correlation of DNA is 1.00, RNA is 0.98 and DNA/RNA ratio is 0.96.

DNA over RNA counts

Plotting normalized counts of DNA vs RNA (median across replicates). Only oligos within all replicates are shown. We should see a variation within the RNA count data (along the y axis). If count data between RNA and DNA is highly correlated (e.g. follows the identity line) there is no variation between designed oligos. This is an indication that RNA is inflated with DNA and the DNA digestion before creating cDNA did not work as expected.

Oligo correlation

Oligo correlation plots of DNA, RNA and DNA/RNA ratios across replicates. First tab shows plots using (in average) 2302 oligos with a minimum number of 10 barcodes. Second tab shows all 2391 oligos that have assigned barcodes.

Condition A B #Oligos A #Oligos B #Oligos Joined DNA spearman RNA spearman Ratio spearman DNA log2 pearson RNA log2 pearson Ratio log2 pearson
HEPG2 1 2 2303 2302 2302 1.00 0.98 0.96 1.00 0.98 0.96
HEPG2 1 3 2303 2303 2303 1.00 0.98 0.97 1.00 0.98 0.97
HEPG2 2 3 2302 2303 2302 1.00 1.00 0.99 1.00 1.00 0.99
Condition A B #Oligos A #Oligos B #Oligos Joined DNA spearman RNA spearman Ratio spearman DNA log2 pearson RNA log2 pearson Ratio log2 pearson
HEPG2 1 2 2391 2391 2391 0.99 0.98 0.96 0.99 0.98 0.95
HEPG2 1 3 2391 2391 2391 0.99 0.98 0.97 0.99 0.98 0.97
HEPG2 2 3 2391 2391 2391 0.99 0.99 0.99 0.99 0.99 0.98

Experiment statistic

The total number of oligos in this experiment is 2398 (defined by the assignment) with 938503 associated barcodes.

In average across replicates we see 2391 from 458815 average barcodes in the count data and around 377427 barcodes where not in the assignment.

condition replicate oligos dna/rna matched barcodes unknown barcodes dna/rna % matched barcodes total dna counts total rna counts avg dna counts per bc avg rna counts per bc barcode outlier removed avg dna/rna barcodes per oligo
HEPG2 1 2391 458254 376620 54.89 21004761 55171411 25.16 66.08 0 191.66
HEPG2 2 2391 455257 295377 60.65 20013665 36062289 26.66 48.04 0 190.40
HEPG2 3 2391 462933 460283 50.14 29614890 55689543 32.08 60.32 0 193.61
Experiment Barcodes Counts Average counts Assigned barcodes Assigned counts Average assigned counts Fraction assigned barcodes Fraction assigned counts
HEPG2_1_DNA 1712608 21963588 12.82 469619 17029932 36.26 0.27 0.78
HEPG2_2_DNA 1643652 20988652 12.77 467754 16298931 34.85 0.28 0.78
HEPG2_3_DNA 2111501 30931153 14.65 477876 24015191 50.25 0.23 0.78
HEPG2_1_RNA 2778818 57511408 20.70 487102 43587667 89.48 0.18 0.76
HEPG2_2_RNA 2198428 37761946 17.18 482090 28544055 59.21 0.22 0.76
HEPG2_3_RNA 2777175 57875595 20.84 487794 43863941 89.92 0.18 0.76

Number of barcodes per oligo

Histogramm of number of barcodes per oligo. Median is blue, mean is red.

Activity

Violin and box plots of the log2 fold change of all oligos by the assay. Grouped by labels if set, otherwise NA. First tab shows plots using (in average) 2302 oligos with a minimum number of 10 barcodes. Second tab shows all 2391 oligos that have assigned barcodes.